INFERRING BIOLOGICAL PATHWAYS FROM UNSTRUCTURED TEXT ANALYSIS

摘要

A biological pathway is a series of actions that take place in an organism that lead to some resulting pathology or otherwise change the organism state. In the cell, these actions typically take place between molecules called proteins. Proteins within the cell interact in ways that are not fully understood, but evidence concerning these interactions is constantly being collected and published by microbiologists. The disclosed method automatically infers such biological pathways between proteins by looking at the overall system of published literature about those proteins.

主权项

1. A method for discovering a pathway among a set of biological and/or chemical entities, comprising:
a) providing documents about each of the biological and/or chemical entities; b) creating a vector space representation of the documents based on words and/or phrases occurring in the documents; c) for each biological and/or chemical entity, creating a centroid in the vector space based on the vectors corresponding to documents mentioning that biological and/or chemical entity; d) creating a relative distance network of the biological and/or chemical entities, in view of the centroids, thereby identifying a particular pathway connecting the centroids; and e) finding at least one most connected centroid on said particular pathway, thereby identifying a particular biological and/or chemical entity for further investigation, wherein said particular biological and/or chemical entity corresponds to said at least one most connected centroid.